No. 3DS in DS mode cannot access GBA slot, cannot switch cards once the ROM has been booted (eepinator and nitrohax wont work) and cannot flash a custom firmware on (hbfirmware or flashme). Other than those limitations, it should perform without much difference, aside from the screen filter to stretch the resolution.

Other than those limitations, it should perform without much difference, aside from the screen filter to stretch the resolution.

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It zooms the resolution, not stretch. It uses black borders to keep the aspect ratio correct (which it wouldn't be if it was stretched). And you can disable the zoom by holding start and/or select when launching DS mode (and then there's even more black borders). On a 3DSXL that mode is pretty much the same size as on an original DS.